sanger/sequencescape

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app/models/sequencing_pipeline.rb

Summary

Maintainability
A
1 hr
Test Coverage
A
97%

SequencingPipeline#detach_request_from_batch has approx 7 statements
Open

  def detach_request_from_batch(batch, request)
Severity: Minor
Found in app/models/sequencing_pipeline.rb by reek

A method with Too Many Statements is any method that has a large number of lines.

Too Many Statements warns about any method that has more than 5 statements. Reek's smell detector for Too Many Statements counts +1 for every simple statement in a method and +1 for every statement within a control structure (if, else, case, when, for, while, until, begin, rescue) but it doesn't count the control structure itself.

So the following method would score +6 in Reek's statement-counting algorithm:

def parse(arg, argv, &error)
  if !(val = arg) and (argv.empty? or /\A-/ =~ (val = argv[0]))
    return nil, block, nil                                         # +1
  end
  opt = (val = parse_arg(val, &error))[1]                          # +2
  val = conv_arg(*val)                                             # +3
  if opt and !arg
    argv.shift                                                     # +4
  else
    val[0] = nil                                                   # +5
  end
  val                                                              # +6
end

(You might argue that the two assigments within the first @if@ should count as statements, and that perhaps the nested assignment should count as +2.)

SequencingPipeline#is_read_length_consistent_for_batch? has approx 6 statements
Open

  def is_read_length_consistent_for_batch?(batch) # rubocop:todo Metrics/AbcSize
Severity: Minor
Found in app/models/sequencing_pipeline.rb by reek

A method with Too Many Statements is any method that has a large number of lines.

Too Many Statements warns about any method that has more than 5 statements. Reek's smell detector for Too Many Statements counts +1 for every simple statement in a method and +1 for every statement within a control structure (if, else, case, when, for, while, until, begin, rescue) but it doesn't count the control structure itself.

So the following method would score +6 in Reek's statement-counting algorithm:

def parse(arg, argv, &error)
  if !(val = arg) and (argv.empty? or /\A-/ =~ (val = argv[0]))
    return nil, block, nil                                         # +1
  end
  opt = (val = parse_arg(val, &error))[1]                          # +2
  val = conv_arg(*val)                                             # +3
  if opt and !arg
    argv.shift                                                     # +4
  else
    val[0] = nil                                                   # +5
  end
  val                                                              # +6
end

(You might argue that the two assigments within the first @if@ should count as statements, and that perhaps the nested assignment should count as +2.)

SequencingPipeline#is_flowcell_type_consistent_for_batch? has approx 6 statements
Open

  def is_flowcell_type_consistent_for_batch?(batch) # rubocop:todo Metrics/AbcSize
Severity: Minor
Found in app/models/sequencing_pipeline.rb by reek

A method with Too Many Statements is any method that has a large number of lines.

Too Many Statements warns about any method that has more than 5 statements. Reek's smell detector for Too Many Statements counts +1 for every simple statement in a method and +1 for every statement within a control structure (if, else, case, when, for, while, until, begin, rescue) but it doesn't count the control structure itself.

So the following method would score +6 in Reek's statement-counting algorithm:

def parse(arg, argv, &error)
  if !(val = arg) and (argv.empty? or /\A-/ =~ (val = argv[0]))
    return nil, block, nil                                         # +1
  end
  opt = (val = parse_arg(val, &error))[1]                          # +2
  val = conv_arg(*val)                                             # +3
  if opt and !arg
    argv.shift                                                     # +4
  else
    val[0] = nil                                                   # +5
  end
  val                                                              # +6
end

(You might argue that the two assigments within the first @if@ should count as statements, and that perhaps the nested assignment should count as +2.)

Complex method SequencingPipeline#is_flowcell_type_consistent_for_batch? (25.5)
Open

  def is_flowcell_type_consistent_for_batch?(batch) # rubocop:todo Metrics/AbcSize
    if (batch.requests.size == 0) || (batch.requests.first.request_metadata.nil?)
      # No requests selected or the pipeline doesn't contain metadata to check
      return true
    end
Severity: Minor
Found in app/models/sequencing_pipeline.rb by flog

Flog calculates the ABC score for methods. The ABC score is based on assignments, branches (method calls), and conditions.

You can read more about ABC metrics or the flog tool

Complex method SequencingPipeline#is_read_length_consistent_for_batch? (25.5)
Open

  def is_read_length_consistent_for_batch?(batch) # rubocop:todo Metrics/AbcSize
    if (batch.requests.size == 0) || (batch.requests.first.request_metadata.nil?)
      # No requests selected or the pipeline doesn't contain metadata to check
      return true
    end
Severity: Minor
Found in app/models/sequencing_pipeline.rb by flog

Flog calculates the ABC score for methods. The ABC score is based on assignments, branches (method calls), and conditions.

You can read more about ABC metrics or the flog tool

SequencingPipeline#is_read_length_consistent_for_batch? calls 'read_length_list.size' 2 times
Open

    return true if read_length_list.size == 0

    # There are some requests that don't have the read_length_attribute
    return false if read_length_list.size != batch.requests.size
Severity: Minor
Found in app/models/sequencing_pipeline.rb by reek

Duplication occurs when two fragments of code look nearly identical, or when two fragments of code have nearly identical effects at some conceptual level.

Reek implements a check for Duplicate Method Call.

Example

Here's a very much simplified and contrived example. The following method will report a warning:

def double_thing()
  @other.thing + @other.thing
end

One quick approach to silence Reek would be to refactor the code thus:

def double_thing()
  thing = @other.thing
  thing + thing
end

A slightly different approach would be to replace all calls of double_thing by calls to @other.double_thing:

class Other
  def double_thing()
    thing + thing
  end
end

The approach you take will depend on balancing other factors in your code.

SequencingPipeline#is_flowcell_type_consistent_for_batch? calls 'flowcell_type_list.size' 2 times
Open

    return true if flowcell_type_list.size == 0

    # There are some requests that don't have the requested_flowcell_type
    return false if flowcell_type_list.size != batch.requests.size
Severity: Minor
Found in app/models/sequencing_pipeline.rb by reek

Duplication occurs when two fragments of code look nearly identical, or when two fragments of code have nearly identical effects at some conceptual level.

Reek implements a check for Duplicate Method Call.

Example

Here's a very much simplified and contrived example. The following method will report a warning:

def double_thing()
  @other.thing + @other.thing
end

One quick approach to silence Reek would be to refactor the code thus:

def double_thing()
  thing = @other.thing
  thing + thing
end

A slightly different approach would be to replace all calls of double_thing by calls to @other.double_thing:

class Other
  def double_thing()
    thing + thing
  end
end

The approach you take will depend on balancing other factors in your code.

SequencingPipeline#is_read_length_consistent_for_batch? calls 'batch.requests' 4 times
Open

    if (batch.requests.size == 0) || (batch.requests.first.request_metadata.nil?)
      # No requests selected or the pipeline doesn't contain metadata to check
      return true
    end

Severity: Minor
Found in app/models/sequencing_pipeline.rb by reek

Duplication occurs when two fragments of code look nearly identical, or when two fragments of code have nearly identical effects at some conceptual level.

Reek implements a check for Duplicate Method Call.

Example

Here's a very much simplified and contrived example. The following method will report a warning:

def double_thing()
  @other.thing + @other.thing
end

One quick approach to silence Reek would be to refactor the code thus:

def double_thing()
  thing = @other.thing
  thing + thing
end

A slightly different approach would be to replace all calls of double_thing by calls to @other.double_thing:

class Other
  def double_thing()
    thing + thing
  end
end

The approach you take will depend on balancing other factors in your code.

SequencingPipeline#is_flowcell_type_consistent_for_batch? calls 'batch.requests.size' 2 times
Open

    if (batch.requests.size == 0) || (batch.requests.first.request_metadata.nil?)
      # No requests selected or the pipeline doesn't contain metadata to check
      return true
    end

Severity: Minor
Found in app/models/sequencing_pipeline.rb by reek

Duplication occurs when two fragments of code look nearly identical, or when two fragments of code have nearly identical effects at some conceptual level.

Reek implements a check for Duplicate Method Call.

Example

Here's a very much simplified and contrived example. The following method will report a warning:

def double_thing()
  @other.thing + @other.thing
end

One quick approach to silence Reek would be to refactor the code thus:

def double_thing()
  thing = @other.thing
  thing + thing
end

A slightly different approach would be to replace all calls of double_thing by calls to @other.double_thing:

class Other
  def double_thing()
    thing + thing
  end
end

The approach you take will depend on balancing other factors in your code.

SequencingPipeline#is_read_length_consistent_for_batch? calls 'batch.requests.size' 2 times
Open

    if (batch.requests.size == 0) || (batch.requests.first.request_metadata.nil?)
      # No requests selected or the pipeline doesn't contain metadata to check
      return true
    end

Severity: Minor
Found in app/models/sequencing_pipeline.rb by reek

Duplication occurs when two fragments of code look nearly identical, or when two fragments of code have nearly identical effects at some conceptual level.

Reek implements a check for Duplicate Method Call.

Example

Here's a very much simplified and contrived example. The following method will report a warning:

def double_thing()
  @other.thing + @other.thing
end

One quick approach to silence Reek would be to refactor the code thus:

def double_thing()
  thing = @other.thing
  thing + thing
end

A slightly different approach would be to replace all calls of double_thing by calls to @other.double_thing:

class Other
  def double_thing()
    thing + thing
  end
end

The approach you take will depend on balancing other factors in your code.

SequencingPipeline#is_flowcell_type_consistent_for_batch? calls 'batch.requests' 4 times
Open

    if (batch.requests.size == 0) || (batch.requests.first.request_metadata.nil?)
      # No requests selected or the pipeline doesn't contain metadata to check
      return true
    end

Severity: Minor
Found in app/models/sequencing_pipeline.rb by reek

Duplication occurs when two fragments of code look nearly identical, or when two fragments of code have nearly identical effects at some conceptual level.

Reek implements a check for Duplicate Method Call.

Example

Here's a very much simplified and contrived example. The following method will report a warning:

def double_thing()
  @other.thing + @other.thing
end

One quick approach to silence Reek would be to refactor the code thus:

def double_thing()
  thing = @other.thing
  thing + thing
end

A slightly different approach would be to replace all calls of double_thing by calls to @other.double_thing:

class Other
  def double_thing()
    thing + thing
  end
end

The approach you take will depend on balancing other factors in your code.

Complex method SequencingPipeline#detach_request_from_batch (21.9)
Open

  def detach_request_from_batch(batch, request)
    request.fail!

    # Note that the request metadata also needs to be cloned for this to work.
    ActiveRecord::Base.transaction do
Severity: Minor
Found in app/models/sequencing_pipeline.rb by flog

Flog calculates the ABC score for methods. The ABC score is based on assignments, branches (method calls), and conditions.

You can read more about ABC metrics or the flog tool

SequencingPipeline#on_start_batch doesn't depend on instance state (maybe move it to another class?)
Open

  def on_start_batch(batch, user)
Severity: Minor
Found in app/models/sequencing_pipeline.rb by reek

A Utility Function is any instance method that has no dependency on the state of the instance.

SequencingPipeline#post_release_batch doesn't depend on instance state (maybe move it to another class?)
Open

  def post_release_batch(batch, _user)
Severity: Minor
Found in app/models/sequencing_pipeline.rb by reek

A Utility Function is any instance method that has no dependency on the state of the instance.

SequencingPipeline#is_flowcell_type_consistent_for_batch? doesn't depend on instance state (maybe move it to another class?)
Open

  def is_flowcell_type_consistent_for_batch?(batch) # rubocop:todo Metrics/AbcSize
Severity: Minor
Found in app/models/sequencing_pipeline.rb by reek

A Utility Function is any instance method that has no dependency on the state of the instance.

SequencingPipeline#is_flowcell_type_consistent_for_batch? performs a nil-check
Open

    if (batch.requests.size == 0) || (batch.requests.first.request_metadata.nil?)
Severity: Minor
Found in app/models/sequencing_pipeline.rb by reek

A NilCheck is a type check. Failures of NilCheck violate the "tell, don't ask" principle.

Additionally, type checks often mask bigger problems in your source code like not using OOP and / or polymorphism when you should.

Example

Given

class Klass
  def nil_checker(argument)
    if argument.nil?
      puts "argument isn't nil!"
    end
  end
end

Reek would emit the following warning:

test.rb -- 1 warning:
  [3]:Klass#nil_checker performs a nil-check. (NilCheck)

SequencingPipeline#detach_request_from_batch doesn't depend on instance state (maybe move it to another class?)
Open

  def detach_request_from_batch(batch, request)
Severity: Minor
Found in app/models/sequencing_pipeline.rb by reek

A Utility Function is any instance method that has no dependency on the state of the instance.

SequencingPipeline#is_read_length_consistent_for_batch? performs a nil-check
Open

    if (batch.requests.size == 0) || (batch.requests.first.request_metadata.nil?)
Severity: Minor
Found in app/models/sequencing_pipeline.rb by reek

A NilCheck is a type check. Failures of NilCheck violate the "tell, don't ask" principle.

Additionally, type checks often mask bigger problems in your source code like not using OOP and / or polymorphism when you should.

Example

Given

class Klass
  def nil_checker(argument)
    if argument.nil?
      puts "argument isn't nil!"
    end
  end
end

Reek would emit the following warning:

test.rb -- 1 warning:
  [3]:Klass#nil_checker performs a nil-check. (NilCheck)

SequencingPipeline#is_read_length_consistent_for_batch? doesn't depend on instance state (maybe move it to another class?)
Open

  def is_read_length_consistent_for_batch?(batch) # rubocop:todo Metrics/AbcSize
Severity: Minor
Found in app/models/sequencing_pipeline.rb by reek

A Utility Function is any instance method that has no dependency on the state of the instance.

Similar blocks of code found in 2 locations. Consider refactoring.
Open

  def is_read_length_consistent_for_batch?(batch) # rubocop:todo Metrics/AbcSize
    if (batch.requests.size == 0) || (batch.requests.first.request_metadata.nil?)
      # No requests selected or the pipeline doesn't contain metadata to check
      return true
    end
Severity: Minor
Found in app/models/sequencing_pipeline.rb and 1 other location - About 55 mins to fix
app/models/sequencing_pipeline.rb on lines 35..49

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 46.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

  def is_flowcell_type_consistent_for_batch?(batch) # rubocop:todo Metrics/AbcSize
    if (batch.requests.size == 0) || (batch.requests.first.request_metadata.nil?)
      # No requests selected or the pipeline doesn't contain metadata to check
      return true
    end
Severity: Minor
Found in app/models/sequencing_pipeline.rb and 1 other location - About 55 mins to fix
app/models/sequencing_pipeline.rb on lines 18..32

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 46.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

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